(RNA-seq) All cells were harvested in Trizol and total RNA was extracted using Direct-Zol RNA mini-prep kit (zymo research) according to manufacturer's protocol. (ChIP-seq) A253 and SCC25 cells were grown to 80% confluency in 150 mm culture dish and cross-linked with 1% Formaldehyde for 10 minutes. The cross-linking reaction was quenched with Glycine to a final concentration of 125mM. Fixed HNSCC cells were prepared for chromatin shearing using Diagenode low Sodium Dodecyl Sulphate (SDS) shearing kit for Transcription Factors (Diagenode) and sonicated using a Diagenode Bioruptor to obtain sheared chromatin of between 200-400bp. p63 ChIP for A253 cells was performed using 2ug anti-p63 antibodies (Np631.1, and 4A4). SCC25 ChIP was performed using 2ug H129 or 3ug 4A4 antibodies. The p63 4A4 experiment in SCC25 has been previously described [37, 102]. Following immunoprecipitation, DNA-protein complex was then subjected to cross-link reversal and proteinase K treatment. Input DNA and DNA from immunoprecipitation experiments were purified and concentrated using Qiagen MinElute kit. (RNA-seq) Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Total RNA was enriched for mRNA before library construction (ChIP-seq) DNA libraries were prepared from concentrated DNA using ThruPLEX DNA-seq kit (Rubicon Genomics), and single-end sequencing was done on an Illumina HISeq 2500.